Carbon isotope stratigraphic records across the Triassic-Jurassic (Tr-J) boundary show carbon isotope excursions in both marine and terrestrial sections, indicating frequent perturbations of the global carbon cycles, which are linked to the ~600 kyr pulsed emplacement of the Central Atlantic Magmatic Province (CAMP). However, few detailed carbon isotope stratigraphic reports from high-latitude terrestrial deposition have been documented in contrast to the contemporaneous low- to mid-latitude records. It hampers the understanding of the climatic response in the high-latitude terrestrial areas and the modeling global carbon cycles triggered by CAMP volcanisms. Here, we present high-resolution organic carbon isotope data primarily originated from C3 plants in the Haojiagou section in the paleo-high-latitude Junggar Basin, NW China. Combined with previously published biostratigraphic and geochemical results, carbon isotope stratigraphy with distinct “initial negative carbon isotope excursions” (I-CIE) and “main negative carbon isotope excursions” (M-CIE) is built in the Junggar Basin and allows a global stratigraphic correlation. The end-Triassic mass extinction (ETE) and the Tr-J boundary is then well identified. The excursion magnitude is similar to that in Greenland and Poland where the sections are also terrestrial. Climatic pattern recorded in the Junggar Basin rapidly changed across the Tr-J transition and coincides with a bloom of fern spores, increased wildfire activities, enhanced hydrological cycles and soil loss.